But, then i have 3 different runs for the same system, each 200ns. Is it
incorrect to say that the system has experienced conformational sampling
for a total of 600ns, which might be long enough for loops?
Asmita
On Mon, Sep 1, 2014 at 5:54 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Mon, Sep 01, 2014, Asmita Gupta wrote:
> >
> > In 2 out of 3 trajectories, the structure is experiencing a loop residue
> > backbone flipping (zeta, chi and delta), after which it remains stable.
> > However, with parmbsc0, this residue flipping is not observed at all,
> > neither with YIL chi correction.
>
> One useful analysis is to see how long it took for the flip to take place
> in
> the two trajectories where it did happen. If these are significant
> fractions
> of the 200 ns length, then it is plausibly just a matter of chance that you
> did not see such behavior in the third run. You could extend the third run
> longer to see what happens.
>
> >
> > is 200ns enough for a good conformational sampling?
>
> This is not sufficient in general to sample RNA loop configurations.
>
> ....dac
>
>
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Received on Mon Sep 01 2014 - 07:00:02 PDT
